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sestatonsestaton
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add conda wip conda build config
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‎build/conda/build.sh‎

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#!/bin/bash
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#perl ${PREFIX}/bin/cpanm App::Cmd
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#perl Makefile.PL
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#make
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# make test
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#make install
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# PERL_MM_USE_DEFAULT=1 -> automatically answer "yes" on config questions
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PERL_MM_USE_DEFAULT=1 cpan App::cpanminus
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PERL5LIB="" PERL_LOCAL_LIB_ROOT="" PERL_MM_OPT="" PERL_MB_OPT="" perl ${BUILD_PREFIX}/bin/cpanm --installdeps .
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perl Makefile.PL INSTALLDIRS=site
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make
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make install

‎build/conda/conda_environment_HMMER2GO.yml‎

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# conda env create -f conda_environment_HMMER2GO.yml
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name: hmmer2go
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- perl >=5.8
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- perl-bioperl >=1.7
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- perl-clone
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- perl-extutils-makemaker
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- perl-graph
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- perl-lwp-simple
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- perl-lwp-protocol-https
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- perl-json
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- perl-carp
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- perl-sort-naturally
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- perl-list-moreutils
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- perl-file-share
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- perl-file-sharedir-install
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- perl-term-progressbar
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- perl-moose
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- libdb

‎build/conda/deps‎

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perl-ipc-system-simple
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perl-app-cmd
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perl-io-uncompress-gunzip
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perl-io-uncompress-bunzip2
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perl-io-compress-gzip
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perl-io-compress-bzip2
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perl-file-copy
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perl-capture-tiny
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perl-net-ssleay
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perl-io-socket-ssl
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perl-http-tiny
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perl-xml-libxml
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perl-html-tableextract
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perl-bio-db-taxonomy-entrez

‎build/conda/meta.yaml‎

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{% set name = "HMMER2GO" %}
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{% set version = "0.18.2" %}
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package:
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name: {{ name|lower }}
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version: {{ version }}
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source:
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git_url: https://github.com/sestaton/HMMER2GO.git
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git_tag: v{{ version }}
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requirements:
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host:
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- zlib
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- libxml2
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- openssl
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- perl >=5.32
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- perl-bioperl >=1.7.8
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- perl-app-cmd
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- perl-io-uncompress-gunzip
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- perl-io-uncompress-bunzip2
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- perl-capture-tiny
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- perl-net-ssleay
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- perl-io-socket-ssl
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- perl-http-tiny
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- perl-xml-libxml
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- perl-html-tableextract
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- emboss
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- hmmer>=3
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build:
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- make
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- perl >=5.32
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run:
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- perl >=5.32
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- perl-bioperl >=1.7.8
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- perl-app-cmd
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- perl-io-uncompress-gunzip
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- perl-io-uncompress-bunzip2
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- perl-capture-tiny
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- perl-net-ssleay
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- perl-io-socket-ssl
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- perl-http-tiny
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- perl-xml-libxml
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- perl-html-tableextract
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- emboss
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- hmmer>=3
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test:
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source_files:
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- t/test_data
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about:
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home: https://github.com/sestaton/HMMER2GO
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license: MIT
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license_file: LICENSE
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summary: 'Annotate DNA sequences for Gene Ontology terms'
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dev_url: https://github.com/sestaton/HMMER2GO
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doc_url: https://github.com/sestaton/HMMER2GO/wiki
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extra:
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maintainers:
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- Frédéric Chevalier
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- S. Evan Staton

‎build/conda/meta.yaml.bak‎

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{% set name = "HMMER2GO" %}
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{% set version = "0.18.3" %}
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package:
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name: {{ name|lower }}
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version: {{ version }}
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source:
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git_url: https://github.com/sestaton/HMMER2GO.git
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git_tag: v{{ version }}
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requirements:
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host:
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- zlib
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- libxml2
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- openssl
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build:
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- make
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- perl >=5.32
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run:
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- perl >=5.32
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- perl-bioperl >=1.7.8
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- perl-app-cmd
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- perl-io-uncompress-gunzip
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- perl-io-uncompress-bunzip2
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- perl-io-compress-gzip
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- perl-io-compress-bzip2
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- perl-file-copy
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- perl-capture-tiny
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- perl-net-ssleay
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- perl-io-socket-ssl
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- perl-http-tiny
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- perl-xml-libxml
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- perl-html-tableextract
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- perl-bio-db-taxonomy-entrez
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- emboss
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- hmmer>=3
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test:
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source_files:
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- t/test_data
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about:
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home: https://github.com/sestaton/HMMER2GO
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license: MIT
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license_file: LICENSE
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summary: 'Annotate DNA sequences for Gene Ontology terms'
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dev_url: https://github.com/sestaton/HMMER2GO
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doc_url: https://github.com/sestaton/HMMER2GO/wiki
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extra:
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maintainers:
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- Frédéric Chevalier
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- S. Evan Staton

‎build/conda/run_test.sh.bak‎

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#!/bin/bash
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#===========#
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# Variables #
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#===========#
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# Test data directory
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dir="t/test_data/"
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# Pfam file
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pfam2go="$dir/pfam2go"
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# Fasta files
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infile="$dir/t_seqs_nt_gz.fas.gz"
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outorf="$dir/outfile_all"
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# HMM related files
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file=Pfam-A.hmm.gz
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outfile=ftp.ebi.ac.uk//pub/databases/Pfam/current_release/$file
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db="$dir/Pfam-A.hmm"
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# Run related variables
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outfile="$dir/t_orfs_long_Pfam-A.out"
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domtblout="$dir/t_orfs_long_Pfam-A.domtblout"
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tblout="$dir/t_orfs_long_Pfam-A.tblout"
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#======#
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# Test #
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#======#
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# List command
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hmmer2go commands
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# Fetch map
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hmmer2go fetchmap -o "$pfam2go"
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# Get ORF
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hmmer2go getorf -i "$infile" -o "$outorf" -t 0 -a
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[[ $(grep -c ">" "$outorf") -eq 172 ]]
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## Run hmmpress
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## Note: this step downloads the database and uncompresses it. Downloading can be done with either wget or curl but none of them are installed by default and variation between systems exists. It is probably better to not mess with this to avoid failing the test. Alternatively wget or curl could be a dependency.
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# wget ftp://$outfile
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# gunzip -c "$file" > "$flatdb"
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# hmmpress $db
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## Run run
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## Note: this step depends on database generated by hmmpress
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# hmmer2go run -i $infile -d $db -o $tblout
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‎cpanfile‎

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requires 'HTTP::Tiny';
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requires 'XML::LibXML';
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requires 'HTML::TableExtract';
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requires 'Bio::DB::Taxonomy::entrez';
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requires 'Bio::DB::Taxonomy::entrez';
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